Architecture

Loom is an AI research harness for Galaxy bioinformatics, built on Pi.dev. It is deliberately split into a single brain and several thin shells that talk to it over RPC.

Brain and shells

Brain (Loom)                        Shells
────────────                        ──────
extensions/loom/                    bin/loom.js      terminal CLI
  index.ts    extension entry       app/             Orbit (Electron desktop)
  state.ts    session state           src/main/        Node.js main process
  tools.ts    LLM-callable tools       src/renderer/    chat + artifact panes
  context.ts  system prompt          web/             browser shell (LAN, dev)
  notebook-writer.ts  notebook I/O

Loom is the agent brain — the Pi.dev runtime, the system-prompt context, Galaxy invocation tracking, the skills system, and the RPC contract.

Orbit is the Electron desktop shell with a chat + tabbed-artifact layout. The CLI runs the same brain from a terminal. A web shell serves the Orbit renderer over RPC from another device on your LAN. Future shells — a Galaxy-embedded web UI, a hosted server mode — talk to the same brain over the same contract.

The notebook is the state

The durable state is notebook.md. Plans, decisions, results, and interpretation all live as markdown sections inside it; the agent maintains them via standard Edit / Write tools. The only structured side-records are loom-invocation YAML blocks for in-flight Galaxy work. See Concepts.

This keeps Loom aligned with the broader Galaxy ecosystem: Galaxy is the substrate, Page is the shareable artifact, and Loom is one live authoring shell.

Galaxy integration

Galaxy work runs through Galaxy MCP (uvx galaxy-mcp) when credentials are available. During planning the agent surveys the workflow registry and tool catalog, then routes each step to Galaxy or local execution as appropriate.

Tech stack

Built in strict TypeScript on the Pi.dev agent runtime (@earendil-works/pi-coding-agent), bridged to Galaxy through uvx galaxy-mcp. The Orbit desktop shell is Electron (Vite + electron-forge), rendered with marked, in a Galaxy-brand dark theme. Tested with Vitest.

For the engineer-facing deep dive, see docs/architecture.md in the loom repository.